Files updated to v. 1.89, including newly reported samples from Sardinia and the Mediterranean, as well as some not so recent ones I had missed – Mazovian prince, Early Poles – and some updated SNPs of samples from different published papers.

These are some curiously similar SNP inferences around Lake Baikal, apparently N1a1*(xN1a1a), but nevertheless with multiple positives for N1a-L1026 equivalents, showing that this specific lineage (whichever it was) was widespread on both sides of the lake during the Neolithic.

EDIT: According to Pribislav, they are N1a-pre-B187, from Y24317, a rare sister clade of N1a-708. ISOGG 2019 is really far behind new SNPs compared to FTDNA and YFull, and the current nomenclature doesn’t make much sense…

The question is thus if the associated Epigravettian WHG expansion in Western Europe consisted mainly of this subclade, and V2219-associated peoples expanded in a different (later?) wave into SE Europe, or if it was a common L754-rich migration of which we can only see the effects after regional bottlenecks.

Sadly, Iboussieres31-2 has a too small coverage to help support any option.

I have updated the dataset, including reported Neanderthal and Denisovan Y-DNA (ISOGG only).

I have also checked out some of the samples of hg. T. I can’t find Genetiker’s reported SNP for the Varna individual. The best I can do (like the original paper) is CT+.

It’s quite interesting that the R1a-Z93 from the Balkans shows SNP calls similar to the Glăvăneştii one, suggesting that it is an R1a-Z93* sample more closely related to Late Trypillian groups, and thus a potential resurgence event more than a Srubnaya-related migration:

1. I have tested all Baltic Neolithic samples reported as R1b-L754 or P297: all have enough coverage to show they are of basal subclades P297* (xM73, xM269).

2. I also tried using Skoglund et al. (2014) PMDtools with different thresholds to improve damaged samples:

Unsuccessful with the Balkan Chalcolithic outlier from Smyadovo: all positive SNPs except BT are excluded, so we are stuck with the more risky: P-, but R+, R1b+, R1b-M269+ results. For some reason (maybe a specific threshold??) the authors assumed that the R-P280 call was acceptable, though.

Successful with the Samara HG sample: a low threshold (=0.1) confirms one R1b-M73-equivalent SNP, with two negative R1b-M269-equivalent reads, so the most plausible haplogroup seems to be M73, until proven otherwise.

3. I added samples from Egypt, including two newly reported from the Kurchatov Institute (no clear date or location), also the dubious R1b-M269 from the KV 55 coffin and the mtDNA of Djehutynakht in Loreille et al. (2018).

I have left the samples labelled as C2a… according to what I could find in Japanese pages, which suggest they belong to ISOGG 2019 C2b, even though no recent ISOGG nomenclature included them in the past 5 years… These include C2a1a1, C2a1a2, but particularly C2a1a3, whose corresponding C2b1a3?? I couldn’t find anywhere.